FetalBrain - Gestational week associated analysis

Updated: Fri Jan 9 18:09:32 2015

DMR identification with methyl_diff

• Identify DM CpGs
  • methyl_diff one-sided p-value \(\le\) 0.005
    
  • delta fractional methylation \(\ge\) 0.5
    
  • fractional methylation of one sample \(\ge\) 0.75
    
• Collapse DM CpGs into DMRs
  • adjacent DM CpGs have the same DM status;
    
  • distance between adjacent CpGs (size) \(\le\) 300bp;
    
  • No. of CpGs within each DMR \(\ge\) 3.

Background

UMR summary and sanity check

• On average, there are 1692 17-week UMRs, 428 intersect between Cortex and GE, and 450 13-week UMRs, 76 intersect. The intersect is highly significant.
  
• Median DMR length is 321, comparable to breast. It’s similar in all chromosomes in 17-week UMRs, but fluctuate more in 13-week UMRs, probably due to small No. of UMRs identified.
  
• Median No. of CpGs per DMR is 5, also similar to breast.

Sample	Total.DMR	Hyper.DMR	Hypo.DMR
Cortex-HuFNSC02_Cortex-HuFNSC04	1283	179	1104
GE-HuFNSC02_GE-HuFNSC04	3002	722	2280

UMR asymmetry

• On average, there are , 4.8-fold enrichment in total UMR frequency in 17-week compared to 13-week, 8.17 in Cortex, and 3.97 in GE.

GREAT enrichment for GW-associated UMRs

• GREAT terms are strongly associated with neuron differentiation and brain development.
  
• 17-week UMRs are highly enriched in glial cell development in Cortex, and neural tube development in GE. Intersect of these two cell types show enrichment in cell fate commitment related to different types of brain cells.
  
• 13-week UMRs are enriched in neuron fate commitment in Cortex, and regionalization in GE. Intersect of these two cell types show no significant enrichment.

UMR Genomic breakdown

• On average, 62.26% of CpGs in UMRs overlap with genebody, and 23.95% of CpGs in UMRs overlap with promoters, 1.78-fold enriched. 44.87% of CpGs in UMRs overlap with CGIs, 5.97-fold than expected by random.

Proximal UMRs and DE genes

• On average, there are 165 UMRs proximally (TSS +/- 1.5kb) associated with protein-coding genes, 18.23% in 17-week UMRs, and 4.88% in 13-week UMRs, much lower than 17-week UMRs.
  
• Among proximal UMRs, 14.26% of 17-week proximal UMRs are associated with DE genes, 13.64% 13-week UMRs, similar to 17-week UMRs. On average, 20 DE genes are associated with GW UMRs.
  
• Among proximal UMR assocaited with DE genes, 79.55% 17-week UMRs change in the same direction as DE genes (hyper to DN), much higher than any Fetal Brain UMRs and close to observed in breast. 50% in 13-week UMRs, much lower than 17-week UMRs.

	proximal.DMRs	unique.genes	DE.DMRs	unique.DE.genes	same.direction
Cortex04.UMRs	7	7	0	0	0
Cortex02.UMRs	215	215	24	19	21
GE04.UMRs	37	36	6	5	3
GE02.UMRs	402	402	64	57	49

Proximal 13-week UMRs in both Cortex and GE

id	name	description
ENSG00000189334	S100A14	S100_calcium_binding_protein_A14_[Source:HGNC_Symbol;Acc:18901]
ENSG00000237693	IRGM	immunity-related_GTPase_family,M[Source:HGNC_Symbol;Acc:29597]
ENSG00000124564	SLC17A3	solute_carrier_family_17_(sodium_phosphate),member3_[Source:HGNC_Symbol;Acc:10931]

Proximal GE 13-week UMRs with DE genes

id	name	description	DM	DE
ENSG00000134954	ETS1	v-ets_erythroblastosis_virus_E26_oncogene_homolog_1_(avian)_[Source:HGNC_Symbol;Acc:3488]	hyper	UP
ENSG00000136352	NKX2-1	NK2_homeobox_1_[Source:HGNC_Symbol;Acc:11825]	hyper	UP
ENSG00000165588	OTX2	orthodenticle_homeobox_2_[Source:HGNC_Symbol;Acc:8522]	hyper	UP
ENSG00000231421			hyper	DN
ENSG00000155760	FZD7	frizzled_family_receptor_7_[Source:HGNC_Symbol;Acc:4045]	hyper	DN

Proximal 17-week UMRs with DE genes in both Cortex and GE

id	name	description	DM	DE
ENSG00000255737	NA	HCG2014417,isoformCRA_aUncharacterized_proteincDNA_FLJ59598_[Source:UniProtKB/TrEMBL;Acc:B7Z718]	hypo	UP
ENSG00000167178	ISLR2	immunoglobulin_superfamily_containing_leucine-rich_repeat_2_[Source:HGNC_Symbol;Acc:29286]	hypo	UP
ENSG00000161999	JMJD8	jumonji_domain_containing_8_[Source:HGNC_Symbol;Acc:14148]	hypo	UP
ENSG00000051523	CYBA	cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]	hypo	UP
ENSG00000169515	CCDC8	coiled-coil_domain_containing_8_[Source:HGNC_Symbol;Acc:25367]	hypo	UP
ENSG00000205927	OLIG2	oligodendrocyte_lineage_transcription_factor_2_[Source:HGNC_Symbol;Acc:9398]	hypo	UP
ENSG00000189060	H1F0	H1_histone_family,member0_[Source:HGNC_Symbol;Acc:4714]	hypo	UP
ENSG00000146904	EPHA1	EPH_receptor_A1_[Source:HGNC_Symbol;Acc:3385]	hypo	UP
ENSG00000165072	MAMDC2	MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]	hypo	UP

UMRs overlapping with TFBS

TF	UMR17week_Cortex	UMR13week_Cortex	Ratio_Cortex	UMR17week_GE	UMR13week_GE	Ratio_GE
MAZ	133	5	26.6000	319	12	26.5833
GTF2F1	28	1	28.0000	103	2	51.5000
ZBTB7A	97	3	32.3333	201	3	67.0000
HMGN3	66	2	33.0000	131	4	32.7500
NRF1	34	1	34.0000	64	1	64.0000
MXI1	112	3	37.3333	262	7	37.4286
E2F4	50	1	50.0000	110	1	110.0000
CCNT2	87	1	87.0000	148	4	37.0000
E2F6	140	1	140.0000	263	8	32.8750

UMR enrichment at chromosome ends

DE genes summary

• On average, there are 561 genes differentially expressed between 13- and 17-week individuals, NA DE between GW13 and GW15 individuals, NA DE between GW15 and GW17, NA DE between GW13 and GW17.
  
• Within each cell type, majority of DE genes are shared among different comparisons (hypergeometric p-value = 0), less but still significant genes overlap between cell types. .
  
• Majority of the GW-associated DE genes are stage-specific.

	UP	DN	DE	GW	type	Sample
1	284	281	565	GW17-GW15	cortex	GW17-GW15.1_cortex
2	365	165	530	GW17-GW13	cortex	GW17-GW13.1_cortex
3	398	283	681	GW17-GW15	cortex	GW17-GW15.2_cortex
4	497	225	722	GW17-GW13	cortex	GW17-GW13.2_cortex
5	459	183	642	GW15-GW13	cortex	GW15-GW13_cortex
6	587	274	861	GW17-GW15	GE	GW17-GW15.1_GE
7	645	238	883	GW17-GW13	GE	GW17-GW13.1_GE
8	609	312	921	GW17-GW15	GE	GW17-GW15.2_GE
9	610	259	869	GW17-GW13	GE	GW17-GW13.2_GE
10	313	232	545	GW15-GW13	GE	GW15-GW13_GE
11	74	75	173	GW17-GW15	shared	GW17-GW15.1_shared
12	239	65	311	GW17-GW13	shared	GW17-GW13.1_shared
13	78	75	180	GW17-GW15	shared	GW17-GW15.2_shared
14	282	84	372	GW17-GW13	shared	GW17-GW13.2_shared
15	79	74	166	GW15-GW13	shared	GW15-GW13_shared

Stage-specific DE gene profiles

• Cortex stage-specific DE genes are mostly turned on during GW13-GW15, while GE stage-specific DE genes are mostly turned on during GW15-GW17. This supports the clustering in coding gene RPKM, exon RPKM and miRNA RPM that in cortex GW15 clustered with GW17, and in GE GW15 clustered with GW13.

Genes activated during GW13-GW15 in cortex

• ALX3: a transcriptional regulator involved in cell-type differentiation and development. Preferential methylation of this genes promoter is associated with advanced-stage neuroblastoma tumors.
  
• EPHB2: mediate numerous developmental processes, particularly in the nervous system. Functions in axon guidance during development.
  
• FAT2: This protein most likely functions as a cell adhesion molecule, controlling cell proliferation and playing an important role in cerebellum development.
  
• FOSL1: regulators of cell proliferation, differentiation, and transformation. associated with glioblastoma multiforme.
  
• HNF1A: sequence-specific DNA binding transcription factor activity.
  
• LHX4: a transcription factor involved in the control of differentiation and development of the pituitary gland.
  
• MEIS2: essential contributors to developmental programs.
  
• POU5F1: controls the expression of a number of genes involved in embryonic development such as YES1, FGF4, UTF1 and ZFP206. Critical for early embryogenesis and for embryonic stem cell pluripotency.
  
• CDR1: found in some patients with paraneoplastic cerebellar degeneration.
  
• CCKAR: modulates feeding and dopamine-induced behavior in the central and peripheral nervous system.
  
• FOXH1: Transcriptional activator.
  
• LGI1: is rearranged as a result of translocations in glioblastoma cell lines. May play a role in the control of neuroblastoma cell survival.
  
• LHFPL5: In the inner ear, may be a component of the hair cells mechanotransduction machinery.
  
• NEGR1: involved in cell-adhesion. May function as a trans-neural growth-promoting factor in regenerative axon sprouting in the mammalian brain.
  
• NRP2: may play a role in cardiovascular development, axon guidance, and tumorigenesis.
  
• OLIG2: an essential regulator of ventral neuroectodermal progenitor cell fate.
  
• RTN1: May be involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. a specific marker for neurological diseases and cancer.

Genes activated during GW15-GW17 in GE

• ALX3: a transcriptional regulator involved in cell-type differentiation and development. Preferential methylation of this genes promoter is associated with advanced-stage neuroblastoma tumors.
  
• EPHB3: mediate numerous developmental processes, particularly in the nervous system. Functions in axon guidance during development.
  
• GPR98: a G-protein coupled receptor that may have an important role in the development of the central nervous system.
  
• GSX1: Homeobox transcription factor that plays an important role in pituitary development.
  
• HNF1A: sequence-specific DNA binding transcription factor activity.
  
• LHX4: a transcription factor involved in the control of differentiation and development of the pituitary gland.
  
• LHX6: a transcription factor required for the expression of a subset of genes involved in interneurons migration and development.
  
• NKX2-1: a Homeobox transcription factor that activates thyroid specific genes.
  
• SATB2: a Homeobox transcription factor and regulatory determinant of corticocortical connections in the developing cerebral cortex.
  
• SIX3: a Homeobox transcription factor that plays a role in eye development.
  
• SLITRK1: Enhances neurite outgrowth.
  
• SLITRK4: suppress neurite outgrowth.
  
• SLITRK5: suppress neurite outgrowth.
  
• CDR1: found in some patients with paraneoplastic cerebellar degeneration.
  
• CHAT: a characteristic feature of cholinergic neurons, and changes in these neurons may explain some of the symptoms of Alzheimers disease.
  
• DCC: Receptor for netrin required for axon guidance. Mediates axon attraction of neuronal growth cones in the developing nervous system upon ligand binding.
  
• FOXH1: Transcriptional activator.
  
• FOXP4: forkhead box (FOX) transcription factor.
  
• FZD5: Interacts specifically with Wnt5A to induce the beta-catenin pathway.
  
• INA: a member of the intermediate filament family and is involved in the morphogenesis of neurons.
  
• IRX2: a member of the Iroquois homeobox gene family. Members of this family appear to play multiple roles during pattern formation of vertebrate embryos.
  
• NTN1: netrin is thought to be involved in axon guidance and cell migration during development.
  
• NXPH1: forms a very tight complex with alpha neurexins, a group of proteins that promote adhesion between dendrites and axons.
  
• NRGN: a direct target for thyroid hormone in human brain, and that control of expression of this gene could underlay many of the consequences of hypothyroidism on mental states during development.
  
• NRP2: may play a role in cardiovascular development, axon guidance, and tumorigenesis.
  
• OLFM1: May play an important role in regulating the production of neural crest cells by the neural tube.
  
• OLFM3: May play an important role in regulating the production of neural crest cells by the neural tube.
  
• OLIG2: an essential regulator of ventral neuroectodermal progenitor cell fate.
  
• LPPR4: is located in the membranes of outgrowing axons and has been shown to be important for axonal outgrowth during development and regenerative sprouting.
  
• PLXNA2: semaphorin co-receptors. Semaphorins are a large family of secreted or membrane-bound proteins that mediate repulsive effects on axon pathfinding during nervous system development.
  
• SFRP1: soluble modulators of Wnt signaling; epigenetic silencing of SFRP genes leads to deregulated activation of the Wnt-pathway which is associated with cancer.
  
• SLIT1: During neural development involved in axonal navigation at the ventral midline of the neural tube and projection of axons to different regions.
  
• SLIT2: SLIT1 and SLIT2 together seem to be essential for midline guidance in the forebrain by acting as repulsive signal preventing inappropriate midline crossing by axons projecting from the olfactory bulb.
  
• STMN2: plays a regulatory role in neuronal growth and is also thought to be involved in osteogenesis. Reductions in the expression of this gene have been associated with Downs syndrome and Alzheimers disease.
  
• VAX1: homeobox transcription factors that may play an important role in the development of anterior ventral forebrain and visual system.
  
• WNT7A: have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis.
  
• WNT5A: Stimulates cell migration. Decreases proliferation, migration, invasiveness and clonogenicity of carcinoma cells and may act as a tumor suppressor. Mediates motility of melanoma cells. Required during embryogenesis for extension of the primary anterior-posterior axis and for outgrowth of limbs and the genital tubercle.

Stage-specific DE gene shared by Crotex and GE

1. GW13-15:UP, GW15-17:UP;
   No genes
   
2. GW13-15:UP, GW15-17:DN;
   

   id	name	description
   ENSG00000168542	COL3A1	collagen,typeIII,alpha1_[Source:HGNC_Symbol;Acc:2201]
   ENSG00000133636	NTS	neurotensin_[Source:HGNC_Symbol;Acc:8038]
   ENSG00000066032	CTNNA2	catenin_(cadherin-associated_protein),alpha2_[Source:HGNC_Symbol;Acc:2510]
   ENSG00000135063	FAM189A2	family_with_sequence_similarity_189,memberA2_[Source:HGNC_Symbol;Acc:24820]
   ENSG00000214401
   ENSG00000099984	GSTT2	glutathione_S-transferase_theta_2_[Source:HGNC_Symbol;Acc:4642]
   ENSG00000238083	LRRC37A2	leucine_rich_repeat_containing_37,memberA2_[Source:HGNC_Symbol;Acc:32404]
   ENSG00000101255	TRIB3	tribbles_homolog_3_(Drosophila)_[Source:HGNC_Symbol;Acc:16228]
   ENSG00000160284	C21orf56	chromosome_21_open_reading_frame_56_[Source:HGNC_Symbol;Acc:1298]

3. GW13-15:DN, GW15-17:UP;

   id	name	description
   ENSG00000022556	NLRP2	NLR_family,pyrindomain_containing_2_[Source:HGNC_Symbol;Acc:22948]
   ENSG00000225607	NA	Uncharacterized_proteincDNA_FLJ60024,highlysimilar_to_Cytochrome_P450_4F12__[Source:UniProtKB/TrEMBL;Acc:B4DNA9]
   ENSG00000147813	NAPRT1	nicotinate_phosphoribosyltransferase_domain_containing_1_[Source:HGNC_Symbol;Acc:30450]
   ENSG00000167654	ATCAY	ataxia,cerebellar,Cayman_type_[Source:HGNC_Symbol;Acc:779]

4. GW13-15:DN, GW15-17:DN;
   No genes
   
5. GW13-15:UP, GW15-17:not DE;

   id	name	description
   ENSG00000149054	ZNF215	zinc_finger_protein_215_[Source:HGNC_Symbol;Acc:13007]
   ENSG00000215845	TSTD1	thiosulfate_sulfurtransferase_(rhodanese)-like_domain_containing_1_[Source:HGNC_Symbol;Acc:35410]
   ENSG00000100336	APOL4	apolipoprotein_L,4[Source:HGNC_Symbol;Acc:14867]
   ENSG00000163823	CCR1	chemokine_(C-C_motif)receptor1_[Source:HGNC_Symbol;Acc:1602]
   ENSG00000169220	RGS14	regulator_of_G-protein_signaling_14_[Source:HGNC_Symbol;Acc:9996]
   ENSG00000203804	C1orf138	chromosome_1_open_reading_frame_138_[Source:HGNC_Symbol;Acc:32041]
   ENSG00000204520	MICA	MHC_class_I_polypeptide-related_sequence_A_[Source:HGNC_Symbol;Acc:7090]
   ENSG00000080573	COL5A3	collagen,typeV,alpha3_[Source:HGNC_Symbol;Acc:14864]
   ENSG00000165379	LRFN5	leucine_rich_repeat_and_fibronectin_type_III_domain_containing_5_[Source:HGNC_Symbol;Acc:20360]
   ENSG00000213402	PTPRCAP	protein_tyrosine_phosphatase,receptortype,C-associatedprotein_[Source:HGNC_Symbol;Acc:9667]
   ENSG00000139155	SLCO1C1	solute_carrier_organic_anion_transporter_family,member1C1_[Source:HGNC_Symbol;Acc:13819]
   ENSG00000187773	FAM69C	family_with_sequence_similarity_69,memberC_[Source:HGNC_Symbol;Acc:31729]
   ENSG00000133216	EPHB2	EPH_receptor_B2_[Source:HGNC_Symbol;Acc:3393]
   ENSG00000119737	GPR75	G_protein-coupled_receptor_75_[Source:HGNC_Symbol;Acc:4526]
   ENSG00000126790	C14orf149	chromosome_14_open_reading_frame_149_[Source:HGNC_Symbol;Acc:20488]
   ENSG00000162733	DDR2	discoidin_domain_receptor_tyrosine_kinase_2_[Source:HGNC_Symbol;Acc:2731]
   ENSG00000108231	LGI1	leucine-rich,gliomainactivated_1_[Source:HGNC_Symbol;Acc:6572]
   ENSG00000161921	CXCL16	chemokine_(C-X-C_motif)ligand16_[Source:HGNC_Symbol;Acc:16642]
   ENSG00000119673	ACOT2	acyl-CoA_thioesterase_2_[Source:HGNC_Symbol;Acc:18431]
   ENSG00000135046	ANXA1	annexin_A1_[Source:HGNC_Symbol;Acc:533]
   ENSG00000215790	SLC35E2	solute_carrier_family_35,memberE2_[Source:HGNC_Symbol;Acc:20863]
   ENSG00000157150	TIMP4	TIMP_metallopeptidase_inhibitor_4_[Source:HGNC_Symbol;Acc:11823]
   ENSG00000170579	DLGAP1	discs,large(Drosophila)homolog-associatedprotein_1_[Source:HGNC_Symbol;Acc:2905]
   ENSG00000143252	SDHC	succinate_dehydrogenase_complex,subunitC,integralmembrane_protein,15kDa[Source:HGNC_Symbol;Acc:10682]
   ENSG00000107796	ACTA2	actin,alpha2,smoothmuscle,aorta[Source:HGNC_Symbol;Acc:130]
   ENSG00000124193	SRSF6	serine/arginine-rich_splicing_factor_6_[Source:HGNC_Symbol;Acc:10788]
   ENSG00000152661	GJA1	gap_junction_protein,alpha1,43kDa[Source:HGNC_Symbol;Acc:4274]
   ENSG00000184110	EIF3C	eukaryotic_translation_initiation_factor_3,subunitC_[Source:HGNC_Symbol;Acc:3279]

6. GW13-15:DN, GW15-17:not DE;

   id	name	description
   ENSG00000166923	GREM1	gremlin_1_[Source:HGNC_Symbol;Acc:2001]
   ENSG00000164123	C4orf45	chromosome_4_open_reading_frame_45_[Source:HGNC_Symbol;Acc:26342]
   ENSG00000008196	TFAP2B	transcription_factor_AP-2_beta_(activating_enhancer_binding_protein_2_beta)_[Source:HGNC_Symbol;Acc:11743]
   ENSG00000186897	C1QL4	complement_component_1,qsubcomponent-like_4_[Source:HGNC_Symbol;Acc:31416]
   ENSG00000054598	FOXC1	forkhead_box_C1_[Source:HGNC_Symbol;Acc:3800]
   ENSG00000104808	DHDH	dihydrodiol_dehydrogenase_(dimeric)_[Source:HGNC_Symbol;Acc:17887]
   ENSG00000124813	RUNX2	runt-related_transcription_factor_2_[Source:HGNC_Symbol;Acc:10472]
   ENSG00000173068	BNC2	basonuclin_2_[Source:HGNC_Symbol;Acc:30988]
   ENSG00000165929	TC2N	tandem_C2_domains,nuclear[Source:HGNC_Symbol;Acc:19859]
   ENSG00000157064	NMNAT2	nicotinamide_nucleotide_adenylyltransferase_2_[Source:HGNC_Symbol;Acc:16789]
   ENSG00000243244	STON1	stonin_1_[Source:HGNC_Symbol;Acc:17003]
   ENSG00000173809	TDRD12	tudor_domain_containing_12_[Source:HGNC_Symbol;Acc:25044]
   ENSG00000135333	EPHA7	EPH_receptor_A7_[Source:HGNC_Symbol;Acc:3390]
   ENSG00000231421
   ENSG00000168675	C18orf1	chromosome_18_open_reading_frame_1_[Source:HGNC_Symbol;Acc:1224]
   ENSG00000156395	SORCS3	sortilin-related_VPS10_domain_containing_receptor_3_[Source:HGNC_Symbol;Acc:16699]
   ENSG00000204103	MAFB	v-maf_musculoaponeurotic_fibrosarcoma_oncogene_homolog_B_(avian)_[Source:HGNC_Symbol;Acc:6408]
   ENSG00000168447	SCNN1B	sodium_channel,nonvoltage-gated1,beta[Source:HGNC_Symbol;Acc:10600]
   ENSG00000106546	AHR	aryl_hydrocarbon_receptor_[Source:HGNC_Symbol;Acc:348]
   ENSG00000117598	NA	Lipid_phosphate_phosphatase-related_protein_type_5_[Source:UniProtKB/Swiss-Prot;Acc:Q32ZL2]
   ENSG00000120322	PCDHB8	protocadherin_beta_8_[Source:HGNC_Symbol;Acc:8693]
   ENSG00000250305	NA	Putative_methyltransferase_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q9P272]
   ENSG00000106868	SUSD1	sushi_domain_containing_1_[Source:HGNC_Symbol;Acc:25413]
   ENSG00000183943	PRKX	protein_kinase,X-linked[Source:HGNC_Symbol;Acc:9441]
   ENSG00000204060	FOXO6	forkhead_box_O6_[Source:HGNC_Symbol;Acc:24814]
   ENSG00000170941	NA	Uncharacterized_protein_KIAA1456_[Source:UniProtKB/Swiss-Prot;Acc:Q8N9K7]
   ENSG00000063438	AHRR	aryl-hydrocarbon_receptor_repressor_[Source:HGNC_Symbol;Acc:346]
   ENSG00000107902	LHPP	phospholysine_phosphohistidine_inorganic_pyrophosphate_phosphatase_[Source:HGNC_Symbol;Acc:30042]
   ENSG00000169436	COL22A1	collagen,typeXXII,alpha1_[Source:HGNC_Symbol;Acc:22989]
   ENSG00000184985	SORCS2	sortilin-related_VPS10_domain_containing_receptor_2_[Source:HGNC_Symbol;Acc:16698]
   ENSG00000163328	GPR155	G_protein-coupled_receptor_155_[Source:HGNC_Symbol;Acc:22951]
   ENSG00000173598	NUDT4	nudix_(nucleoside_diphosphate_linked_moiety_X)-type_motif_4_[Source:HGNC_Symbol;Acc:8051]
   ENSG00000114200	BCHE	butyrylcholinesterase_[Source:HGNC_Symbol;Acc:983]
   ENSG00000183722	LHFP	lipoma_HMGIC_fusion_partner_[Source:HGNC_Symbol;Acc:6586]
   ENSG00000139722	VPS37B	vacuolar_protein_sorting_37_homolog_B_(S.cerevisiae)[Source:HGNC_Symbol;Acc:25754]

7. GW13-15:not DE, GW15-17:UP;

   id	name	description
   ENSG00000145247	OCIAD2	OCIA_domain_containing_2_[Source:HGNC_Symbol;Acc:28685]
   ENSG00000070748	CHAT	choline_O-acetyltransferase_[Source:HGNC_Symbol;Acc:1912]
   ENSG00000165659	DACH1	dachshund_homolog_1_(Drosophila)_[Source:HGNC_Symbol;Acc:2663]
   ENSG00000165983	PTER	phosphotriesterase_related_[Source:HGNC_Symbol;Acc:9590]
   ENSG00000139220	PPFIA2	protein_tyrosine_phosphatase,receptortype,fpolypeptide_(PTPRF),interactingprotein_(liprin),alpha2_[Source:HGNC_Symbol;Acc:9246]
   ENSG00000147255	IGSF1	immunoglobulin_superfamily,member1_[Source:HGNC_Symbol;Acc:5948]
   ENSG00000146233	CYP39A1	cytochrome_P450,family39,subfamilyA,polypeptide1_[Source:HGNC_Symbol;Acc:17449]
   ENSG00000181649	PHLDA2	pleckstrin_homology-like_domain,familyA,member2_[Source:HGNC_Symbol;Acc:12385]
   ENSG00000204516	MICB	MHC_class_I_polypeptide-related_sequence_B_[Source:HGNC_Symbol;Acc:7091]
   ENSG00000164692	COL1A2	collagen,typeI,alpha2_[Source:HGNC_Symbol;Acc:2198]
   ENSG00000114805	PLCH1	phospholipase_C,eta1_[Source:HGNC_Symbol;Acc:29185]
   ENSG00000051523	CYBA	cytochrome_b-245,alphapolypeptide_[Source:HGNC_Symbol;Acc:2577]
   ENSG00000145703	IQGAP2	IQ_motif_containing_GTPase_activating_protein_2_[Source:HGNC_Symbol;Acc:6111]
   ENSG00000165072	MAMDC2	MAM_domain_containing_2_[Source:HGNC_Symbol;Acc:23673]
   ENSG00000130558	OLFM1	olfactomedin_1_[Source:HGNC_Symbol;Acc:17187]
   ENSG00000120318	ARAP3	ArfGAP_with_RhoGAP_domain,ankyrinrepeat_and_PH_domain_3_[Source:HGNC_Symbol;Acc:24097]
   ENSG00000198750	GATSL2	GATS_protein-like_2_[Source:HGNC_Symbol;Acc:37073]
   ENSG00000162849	KIF26B	kinesin_family_member_26B_[Source:HGNC_Symbol;Acc:25484]
   ENSG00000134333	LDHA	lactate_dehydrogenase_A_[Source:HGNC_Symbol;Acc:6535]
   ENSG00000064666	CNN2	calponin_2_[Source:HGNC_Symbol;Acc:2156]

8. GW13-15:not DE, GW15-17:DN;

   id	name	description
   ENSG00000259210
   ENSG00000198650	TAT	tyrosine_aminotransferase_[Source:HGNC_Symbol;Acc:11573]
   ENSG00000163053	SLC16A14	solute_carrier_family_16,member14_(monocarboxylic_acid_transporter_14)_[Source:HGNC_Symbol;Acc:26417]
   ENSG00000125637	PSD4	pleckstrin_and_Sec7_domain_containing_4_[Source:HGNC_Symbol;Acc:19096]
   ENSG00000153822	KCNJ16	potassium_inwardly-rectifying_channel,subfamilyJ,member16_[Source:HGNC_Symbol;Acc:6262]
   ENSG00000188803	SHISA6	shisa_homolog_6_(Xenopus_laevis)_[Source:HGNC_Symbol;Acc:34491]
   ENSG00000127952	STYXL1	serine/threonine/tyrosine_interacting-like_1_[Source:HGNC_Symbol;Acc:18165]
   ENSG00000150907	FOXO1	forkhead_box_O1_[Source:HGNC_Symbol;Acc:3819]
   ENSG00000076344	RGS11	regulator_of_G-protein_signaling_11_[Source:HGNC_Symbol;Acc:9993]
   ENSG00000174938	SEZ6L2	seizure_related_6_homolog_(mouse)-like_2_[Source:HGNC_Symbol;Acc:30844]
   ENSG00000122694	GLIPR2	GLI_pathogenesis-related_2_[Source:HGNC_Symbol;Acc:18007]
   ENSG00000167774	NDUFA7	NADH_dehydrogenase_(ubiquinone)1alpha_subcomplex,7,14.5kDa_[Source:HGNC_Symbol;Acc:7691]
   ENSG00000132164	SLC6A11	solute_carrier_family_6_(neurotransmitter_transporter,GABA),member_11_[Source:HGNC_Symbol;Acc:11044]

DAVID enrichment for DE genes

• GW associated DE genes shared by cell types show no enrichment due to small gene lists.
  
• GW15 vs GW 13: calcium ion binding in cortex UP and GE DN, neurogenesis in cortex DN.
  
• GW17 vs GW 15: neurogenesis in GE, no enrichment in cortex.
  
• GW17 vs GW 13: calcium ion binding in cortex UP and GE UP, neurogenesis in GE DN.
  

Isoform analysis

• On average, there are NA isoform genes between 13- and 17-week individuals, majority of them are shared among different comparisons and between the two cell types (hypergeometric p-value = 0).
  
• There are 2878 isoform genes in cortex supported by at least two comparisons, and 2505 in GE, among them, 1800 isoform genes are shared between the two cell types.
  
• Isoform genes are enriched in cell signaling related terms.

Sample	DE_genes	DE_exons	with_expressed_genes	isoform_exons	exclude_DE_genes	isoform_genes	GW
Cortex-HuFNSC01_Cortex-HuFNSC03	565	28637	16045	8044	7772	2490	17 vs 15
Cortex-HuFNSC01_Cortex-HuFNSC04	530	27428	13200	6365	6134	2167	17 vs 13
Cortex-HuFNSC02_Cortex-HuFNSC03	681	28963	16765	7961	7630	2425	17 vs 15
Cortex-HuFNSC02_Cortex-HuFNSC04	722	29416	13894	6351	6011	2105	17 vs 13
Cortex-HuFNSC03_Cortex-HuFNSC04	642	26826	12185	5818	5479	1994	15 vs 13
GE-HuFNSC01_GE-HuFNSC03	861	31361	14725	5880	5458	2041	17 vs 15
GE-HuFNSC01_GE-HuFNSC04	883	34359	15889	6401	5996	2049	17 vs 13
GE-HuFNSC02_GE-HuFNSC03	921	32827	15557	5773	5306	1965	17 vs 15
GE-HuFNSC02_GE-HuFNSC04	869	34699	16012	6113	5711	1986	17 vs 13
GE-HuFNSC03_GE-HuFNSC04	545	24752	12223	4582	4422	1454	15 vs 13